Sinister Directive
by 1049
Summary: Normal day, normal fight, just normal. But afterwards, everything takes a turn for the worst as Sonic changes...
1. Chapter 1 Disaster

_ Another day, another battle. That's what the life of Sonic was like. Eggman this, Mephiles that, but he never seemed to grow tired of it. Could it be his undying love for adventure? The will to protect innocents? Or just his cocky personality? No one could know for sure. We all know Sonic, the happy one who wasn't much for violence. Now I wish I could tell you he never changed, whether it was on his own will or not. I wish I could tell you that, but the world is no fairy-tale place._

**_Sinister Directive_**

"Hey Tails, I'm going out, Egghead is up to something again." The young kitsune sighed and continued working on the Tornado.

_He never even asks if I want to help._ Tails thought while working. "Wow, something smells...weird." It was then Tails felt the heat of laying your arm down on a running engine. "FUDGE!"

After fixing up his arm and such, Tails picked up a can of soup from a drawer and began to open it. "I can't shake this feeling. It just feels like I'm not really, cared for." It was true, in some ways. Sonic never asked for help anymore and rarely complimented him, only saved him. Knuckles seemed to just plain ignore him, Shadow was evil to him, he was Shadow though, and all the others, they just seemed the same. "Ah see if I care. I should just ignore it, keep doing my best." Then, an idea popped into Tail's head.

_**Near Emerald Coast**_

"Catch me now!" Sonic ran right up the side of the mountain, Eggman hot on his tail. "Bocoe, Docoe, I'll hold him off, you finish the project."

"Yes sir!" Eggman looked back up at Sonic, only to notice he was gone. "Where did that pest-" Eggman was cut off by a few loud explosions. "For the love of chaos-" a few crumbling boulders fell onto Eggman's machine, crippling many parts of it. Eggman whipped his beat up machine around and looked down at Tails, holding a small glove with rockets attached to it.

"Tails look out!" Sonic shoved Tails out of the way as a missle zoomed past were they were standing. "Sonic! I could've dodged it myself!" Sonic was about to retort when another rain of bullets came flying. Instinctively, Sonic zoomed away from the rock, creating a huge dust cloud. Using this to his advantage, Sonic ran head on at Eggman's machine, spin dashing at the last second. This ripped off a leg to the machine, which could no longer stand. It fell over as Sonic wiped his hands and turned around.

"Now as for Tails... Huh, he must have left."

"I'll get you Sonic if its the last-"

"Doctor, its ready." Eggman snickered as he launched out of his wrecked walker and flew back towards his base. Revenge would be his.

_**Later That Night**_

_Another one of Eggy's machines down, oh yeah! _Sonic thought to himself. The nights were normally cold and dark, but it was especially so tonight.

"Help me!" Whipping around, Sonic listened again. "Someone please help!" Running towards the noise, Sonic found it was coming from an abandoned store. He kicked in the door and walked in. There wasn't much, except for a few empty shelves. Within a second, Sonic was in a choke-hold with a rag over his face, obviously full of chloroform. Before he passed out, Sonic could hear something that sent chills down his spines, a deep, dark voice. "Looks like your mine, now, Hehe."


	2. Chapter 2 First Initiative

Sonic's eyes began to open, everything fuzzy. He let out a deep breath, taking in what he could see. It was a large, black lab. Machines whirred around him. Looking down, Sonic noticed he was strapped to a small bed, cuffs going across his arms and legs. Trying to sit up, a massive headache rushed in, destroying his effort.

"Good, your awake."

Sonic looked to his left to see a figure shrouded in darkness.

"Who the-"

"Now now Sonic, we wouldn't want to use any language here. Now, stand up."

Before Sonic could react, the cuffs popped off and he was brought to a stand. "What, but, how?" The figure began laughing like a maniac.

"Hoho, Sonic. You're too funny. Come here." Sonic walked towards the figure, without even knowing what he was doing. "Legs functioning properly, good. Now, swing your arms."

Sonic did as told, fighting the best as he could. "You sick creep. What are you doing to me?"

The figure stood up, still chuckling. "I now have control over you, thanks to a small chip embedded in your brain. You will do as I say. Don't even try to disobey, or I will take your conscience away too, and you won't even have any memory of anything."

Sonic spit right in the figure's eye, trying desperately to escape. The figure wiped the spit away, and pulled out a small laptop. "You asked for it."

Suddenly, Sonic's mind went blank. The figure was now in complete control. "From now on, call me the Director, seeing as how I will be directing the upcoming events." The Director had a smirk on.

"Time for your first directive. You are to go to Angel Island and severely wound Knuckles the Echidna. I'll take it one enemy at a time. Hoho!"

Sonic walked out the door, his face showing no emotions. "Orders received. Primary initiative, Knuckles the Echidna."

**_Angel Island_**

It was just an average day for Knuckles, guarding the Master Emerald, keeping away Rouge, the normal. Standing up, Knuckles stretched out as he heard footsteps. "Who goes there!" Knuckles looked down to the bottom of the shrine to see Sonic, staring intently at him. Something was different, something with Sonic.

"Are you OK Sonic?" Before Knuckles could ask more, Sonic sprang up, tackling the echidna.

'What was that for-" Knuckles was cut off by an elbow to the jaw. "You asked for it!"

Charging fist first, Knuckles went to deliver a blow. However Sonic ducked and grabbed Knuckle's waist, flipping him over. Using this momentum, Knuckles sprang back up and delivered a perfect kick to Sonic's chest. Sonic didn't even flinch.

"How the-"

Sonic charged again and shoved Knuckles against a pillar, punching him all the way. Knuckles retaliated with a head-butt, causing a momentary break, which he used to throw Sonic back. Using his speed and strength, Sonic stopped himself, then charged full force and delivered a punch to Knuckles stomach, sending him onto his back.

"OK, OK, I give, just stop!"

Smirking, Sonic grabbed Knuckles neck with one hand, hoisting him into the air. Sonic delivered one final punch to Knuckles' head, knocking him out. The hedgehog tossed Knuckles limp body to the floor, and ran back to the HQ, leaving the bloody echidna for dead.

"Initiative complete, returning to HQ."

The Director let out a deep chuckle as he turned the radio off. "Who's next on my list..."

**_An hour later_**

"Hey Silver, have you seen Sonic?"

"Not since yesterday, sorry Amy." Amy sighed. "Well, thanks anyways."

A wave of sadness hit Amy as she began to worry. Where could he be?" The pink hedgehog decided to walk to Sonic and Tail's house. Hopefully her beloved would be there. Reaching the house not long after, Amy opened the door and shouted.

"Sonic! Tails! Anyone home?" Tails stepped out of the kitchen holding a sandwich. "Oh, its just you Tails." Tails frowned at the comment, but spoke up. "So what's up?"

"Nothing, just looking for Sonic."

"Yeah, I haven't seen him in a while. How about some T.V.?" Tails asked, trying to cheer Amy up.

"That sounds good." Tails flipped on the T.V. as a news reporter came on screen.

"Today, a Knuckles the Echidna was found beaten and left for dead on Angel Island."

Tails nearly choked on his sandwich as Amy gasped. "Turn it up!" Turning up the volume, both listened intently.

"There were no witnesses to the beating, and there are no suspects. The victim was found heavily bruised, bleeding internally, with a concussion and was knocked unconscious, medics say. Somehow, Knuckles survived and is currently being taken care of at the Mobius Emergency Center. It will take months for the victim to even begin to talk again. Anyone with information should-"

Amy flipped off the T.V., not being able to bear anymore.

"Let's go visit Knuckles." Tails nodded as they both headed towards the Tornado.

When they arrived at the Center and found Knuckles, they were both horrified. Knuckles had blood all over, and looked like he had just been hit by a car. There was a steady beat coming from his heart rate monitor. Amy had tears coming down her face as she hugged a crying Tails.

Knuckles didn't make any sounds except for an occasional groan. There was one word he uttered though. "Wait wait wait, repeat that Knuckles." Tails asked.

"...S...So...Son... Sonic..." Both the young fox and hedgehog were shocked. Knuckles' head bobbed to the side as he went back to sleep. "This is not happening, this is not happening! There's no way Sonic would... would he?" Tails just shook his head. "I'm not sure, but its the only lead we have. We have to find Sonic."


End file.
